14. Message in a Bottle

Seven of Nine uses the newly extended range of the starship USS Voyager ' s sensors to locate an unattended network of alien sensor stations. Patching into this, she is able to locate a United Federation of Planets vessel in the Alpha Quadrant. Hoping to contact Starfleet after more than three years in the Delta Quadrant, Voyager ' s crew attempts to send a message along the relay but it is reflected back after degrading en route. Thinking that a holographic signal would not degrade, they send the Doctor, Voyager ' s Emergency Medical Hologram (EMH).

The Doctor arrives in the sickbay of the USS Prometheus, a secret experimental Federation warship. He learns from a dying crewman that the Romulans had learned of the prototype and captured it, killing all on board. Being pursued by the USS Bonchune, the Romulans initiate the first test of the new multi-vector assault mode, in which Prometheus splits into three pieces to engage hostile ships.

Seeking assistance, the Doctor activates the Prometheus ' s EMH (Andy Dick), a Mark II version of the program. The Doctor learns from the other EMH of the Dominion War, which the Federation is fighting in and Romulans have not entered. The second EMH cites protocol for an EMH to deactivate when its vessel is taken over but Voyager ' s doctor notes that they cannot do so as both ships are at risk.

The Romulans do not view EMHs as threats. Using the pretense of an infection on board, the Doctor goes to the bridge to open the atmospheric filters to flood the ship with anesthetizing gas. The ruse fails but when he is captured and interrogated, the Doctor keeps the Romulans stalled long enough for the EMH Mark II to fool the ship's computer into opening the filters, permitting the distribution of the gas. Just after they take control, Prometheus is intercepted by three Romulan D'deridex -class warbirds.

Unfamiliar with the helm and weapons systems, the two EMH programs fail to fool the Romulans into leaving, before three more Starfleet vessels arrive. In the ensuing battle, all six other vessels target Prometheus. The EMH Mark II stumbles upon the command to put the ship into multi-vector assault mode. Prometheus overpowers and destroys one of the Romulan warbirds; the Romulans retreat and a Starfleet security detail arrives aboard.

On Voyager, the crew has learned that the sensor array was not abandoned but is claimed by the Hirogen, who announce themselves and demand that Voyager disconnect at once. Janeway tries to negotiate but the Hirogen officer is recalcitrant. Seven of Nine buys time to await the Doctor's return by stunning the officer with a feedback loop. The Doctor returns via the array with good news; he has briefed Starfleet Headquarters about Voyager, the first time Starfleet has heard from the vessel since it disappeared three years earlier. Voyager has been removed from Starfleet's list of destroyed ships and a message sent back, "You're no longer alone". Starfleet will attempt to help Voyager and will tell next of kin that the crew is alive.